Ultrafast functional profiling of RNA-seq data for nonmodel organisms.

Computational time and cost remain a major bottleneck for RNA-seq data analysis of nonmodel organisms without reference genomes. To address this challenge, we have developed Seq2Fun, a novel, all-in-one, ultrafast tool to directly perform functional quantification of RNA-seq reads without transcriptome de novo assembly. The pipeline starts with raw read quality control: sequencing error correction, removing poly(A) tails, and joining overlapped paired-end reads. It then conducts a DNA-to-protein search by translating each read into all possible amino acid fragments and subsequently identifies possible homologous sequences in a well-curated protein database. Finally, the pipeline generates several informative outputs including gene abundance tables, pathway and species hit tables, an HTML report to visualize the results, and an output of clean reads annotated with mapped genes ready for downstream analysis. Seq2Fun does not have any intermediate steps of file writing and loading, making I/O very efficient. Seq2Fun is written in C++ and can run on a personal computer with a limited number of CPUs and memory. It can process >2,000,000 reads/min and is >120 times faster than conventional workflows based on de novo assembly, while maintaining high accuracy in our various test data sets.

The potential of dietary nanoparticles to enhance allergenicity of milk proteins: an in vitro investigation.

In recent years, the popularity of dietary nanoparticles (NPs) in the food industry as additives has raised concerns because of the lack of knowledge about potential adverse health outcomes ensuing from the interactions of NPs with components of the food matrix and gastrointestinal system. In this study, we used a transwell culture system that consisted of human colorectal adenocarcinoma (Caco-2) cells in the apical insert and Laboratory of Allergic Diseases 2 mast cells in the basal compartment to study the effect of NPs on milk allergen delivery across the epithelial layer, mast cell responses and signaling between epithelial and mast cells in allergenic inflammation. A library of dietary particles (silicon dioxide NPs, titanium dioxide NPs and silver NPs) that varied in particle size, surface chemistry and crystal structures with or without pre-exposure to milk was used in this investigation. Milk-interacted particles were found to acquire surface corona and increased the bioavailability of milk allergens (casein and ß-lactoglobulin) across the intestinal epithelial layer. The signaling between epithelial cells and mast cells resulted in significant changes in the early phase and late-phase activation of the mast cells. This study suggested that antigen challenge in mast cells with the presence of dietary NPs may cause the transition of allergic responses from an immunoglobulin E (IgE)-dependent mechanism to a mixed mechanism (both IgE-dependent and IgE-independent mechanisms).

Associations between mercury exposure with blood pressure and lipid levels: A cross-sectional study of dental professionals.

Mercury (Hg) exposure is a public health problem worldwide that is now being addressed through the Minamata Convention on Mercury. Fish containing methylmercury and dental amalgam containing elemental Hg are the major sources of exposure for most populations. There is some evidence that methylmercury impacts cardiovascular and metabolic health, primarily in populations with high exposure levels. Studies of elemental Hg and these outcomes are relatively rare. We aimed to examine associations between Hg exposure (both elemental and methylmercury) and blood pressure, as well as cholesterol and triglyceride levels. In 2012, we recruited dental professionals attending the Health Screening Program at the American Dental Association (ADA) Annual Session in California. Total Hg levels in hair and blood samples were analyzed as indicators of methylmercury exposure and in urine as an indicator of primarily elemental Hg exposure (n = 386; mean ± sd age 55 ± 11 years). We measured blood pressure (systolic and diastolic) and lipid profiles (total cholesterol, high-density lipoprotein cholesterol [HDL], low-density lipoprotein cholesterol [LDL] and triglycerides). The geometric means (geometric standard deviations) for blood, hair, and urine Hg were 3.64 (2.39) µg/L, 0.60 (2.91) µg/g, and 1.30 (2.44) µg/L, respectively. For every one µg/L increase in specific gravity-adjusted urine Hg, LDL increased by 2.31 mg/dL (95% CI = 0.09, 4.54), in linear regression adjusting for BMI, race, sex, polyunsaturated fatty acid intake from fish consumption, smoking status, and use of cholesterol-lowering medication. No significant associations between Hg biomarkers and blood pressure or hair or blood Hg with lipid levels were observed. Results suggest that elemental Hg exposure may influence LDL concentrations in adults with low-level exposure, and this relationship merits further study in other populations.

Association between heavy metal uptake and growth and reproduction in the anecic earthworm, Alma nilotica (Grube 1855).

Elevated heavy metal concentrations in soils are a cause for concern as they are hazardous to soil organisms including earthworms which are considered as ecosystem engineers. Current ecotoxicity tests predominantly use temperate earthworm species, and thus there is the need to include a broader genera of native species to improve ecological risk assessment. Alma nilotica, is a tropical anecic earthworm species that survives well under laboratory conditions and has potential for use in ecotoxicology testing but lacks published toxicity data for important pollutants. Growth and reproduction bioassays were carried out with A. nilotica to determine the relationship between the concentrations of Cu, Zn, Pb and Cr in spiked soils and their bioaccumulation and toxic effects. Positive linear relationships were found between soil-metal and internal earthworm-metal concentrations. Cu did not inhibit growth up to 35 days of exposure but became toxic with longer exposure duration. Zn was not regulated by A. nilotica although it is an essential metal that is well regulated by Eisenia sp. commonly used in standard ecotoxicity tests, showing differences in metal regulation by earthworms of different ecological categories. Based on bioaccumulation factors (BAFs), growth inhibition and reproduction effects the metals were ranked in decreasing toxicity as Pb > Cr > Zn > Cu. The mean 20% Internal Effects Concentrations (IEC20s) for reproduction were 1.04, 2.9, 8.3 and 224.2 mg metal kg-1 earthworm for Pb, Cr, Zn and Cu respectively. These data can contribute to the improvement of metal risk assessment particularly in tropical contexts.

Factors influencing mercury exposure in Arctic-breeding shorebirds.

Mercury (Hg) pollution remains a concern to Arctic ecosystems, due to long-range transport from southern industrial regions and melting permafrost and glaciers. The objective of this study was to identify intrinsic, extrinsic, and temporal factors influencing Hg concentrations in Arctic-breeding shorebirds and highlight regions and species at greatest risk of Hg exposure. We analyzed 1094 blood and 1384 feather samples from 12 shorebird species breeding at nine sites across the North American Arctic during 2012 and 2013. Blood Hg concentrations, which reflect Hg exposure in the local area in individual shorebirds: 1) ranged from 0.01-3.52 µg/g ww, with an overall mean of 0.30 ± 0.27 µg/g ww; 2) were influenced by species and study site, but not sampling year, with birds sampled near Utqiagvik, AK, having the highest concentrations; and 3) were influenced by foraging habitat at some sites. Feather Hg concentrations, which reflected Hg exposure from the wintering grounds: 1) ranged from 0.07-12.14 µg/g fw in individuals, with an overall mean of 1.14 ± 1.18 µg/g fw; and 2) were influenced by species and year. Most Arctic-breeding shorebirds had blood and feather Hg concentrations at levels where no adverse effects of exposure were predicted, though some individuals sampled near Utqiagvik had Hg levels that would be considered of concern. Overall, these data increase our understanding of how Hg is distributed in the various shorebird breeding areas of the Arctic, what factors predispose Arctic-breeding shorebirds to Hg exposure, and lay the foundation for future monitoring efforts.

FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data.

MOTIVATION: Transcriptomics dose-response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally inefficient and must be locally installed. RESULTS: FastBMD is a web-based tool that implements standardized methods for transcriptomics benchmark dose-response analysis in R. It is >60 times faster than the current leading software, supports transcriptomics data from 13 species, and offers a comprehensive analytical pipeline that goes from processing and normalization of raw gene expression values to interactive exploration of pathway-level benchmark dose results. AVAILABILITY AND IMPLEMENTATION: FastBMD is freely available at www.fastbmd.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hazard Profiling of Commercially Relevant Quantum Dot Components Revealed Synergistic Interactions between Heavy Metals and Polymers.

Commercially used quantum dots (QDs) exemplify complex nanomaterials with multiple components, though little is known about the type of interactions between these components in determining the overall toxicity of this material. We synthesized and characterized a functional QD (CdSe/ZnS_P&E) that was identical in structure and composition to a patented and commercially applied QD and the combinations of its components (CdSe, CdSe/ZnS, ZnS, CdSe_P&E, ZnS_P&E, and P&E). Cells exposed to incremental concentrations of these materials were investigated for cell viability and cellular perturbations, contributing to a final common pathway of cell death using high-content screening assays in model human intestinal epithelial cells (HIEC-6). The concentrations that resulted in a loss of 20% cell viability (EC20 values) for each tested component were used for estimating the combination index (CI) to evaluate synergistic or antagonistic effects between the components. Complete QD (core/shell-polymer) showed the highest toxic potential due to synergistic interactions between core and surface functional groups. The cationic polymer coating enhanced cellular uptake of the QD, ensuing lysosome acidification and release of heavy metal ions to the intracellular milieu, and caused oxidative stress and cytotoxicity. Overall, this study advances our understanding of the collective contribution of individual components of a functional QD toward its toxic potential and emphasizes the need to study multilayered nanomaterials in their entirety for hazard characterization.

Characterizing Variability and Uncertainty Associated with Transcriptomic Dose-Response Modeling.

Transcriptomics dose-response analysis (TDRA) has emerged as a promising approach for integrating toxicogenomics data into a risk assessment context; however, variability and uncertainty associated with experimental design are not well understood. Here, we evaluated n = 55 RNA-seq profiles derived from Japanese quail liver tissue following exposure to chlorpyrifos (0, 0.04, 0.1, 0.2, 0.4, 1, 2, 4, 10, 20, and 40 µg/g; n = 5 replicates per group) via egg injection. The full dataset was subsampled 637 times to generate smaller datasets with different dose ranges and spacing (designs A-E) and number of replicates (n = 2-5). TDRA of the 637 datasets revealed substantial variability in the gene and pathway benchmark doses, but relative stability in overall transcriptomic point-of-departure (tPOD) values when tPODs were calculated with the "pathway" and "mode" methods. Further, we found that tPOD values were more dependent on the dose range and spacing than on the number of replicates, suggesting that optimal experimental designs should use fewer replicates (n = 2 or 3) and more dose groups to reduce uncertainty in the results. Finally, tPOD values ranged by over ten times for all surveyed experimental designs and tPOD types, suggesting that tPODs should be interpreted as order-of-magnitude estimates.

Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay.

There is an urgent demand for more efficient and ethical approaches in ecological risk assessment. Using 17α-ethinylestradiol (EE2) as a model compound, this study established an embryo benchmark dose (BMD) assay for rainbow trout (RBT; Oncorhynchus mykiss) to derive transcriptomic points-of-departure (tPODs) as an alternative to live-animal tests. Embryos were exposed to graded concentrations of EE2 (measured: 0, 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L) from hatch to 4 and up to 60 days post-hatch (dph) to assess molecular and apical responses, respectively. Whole proteome analyses of alevins did not show clear estrogenic effects. In contrast, transcriptomics revealed responses that were in agreement with apical effects, including excessive accumulation of intravascular and hepatic proteinaceous fluid and significant increases in mortality at 55.1 and 169 ng/L EE2 at later time points. Transcriptomic BMD analysis estimated the median of the 20th lowest geneBMD to be 0.18 ng/L, the most sensitive tPOD. Other estimates (0.78, 3.64, and 1.63 ng/L for the 10th percentile geneBMD, first peak geneBMD distribution, and median geneBMD of the most sensitive over-represented pathway, respectively) were within the same order of magnitude as empirically derived apical PODs for EE2 in the literature. This 4-day alternative RBT embryonic assay was effective in deriving tPODs that are protective of chronic effects of EE2.

Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (Pimephales promelas).

There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17α-ethinylestradiol (water control, 0.01% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests.

Lead (Pb) exposure assessment in dried blood spots using Total Reflection X-Ray Fluorescence (TXRF).

Lead (Pb) exposure is often determined through the analysis of whole blood though venipuncture poses ethical, economic, and logistical barriers. Dried Blood Spots (DBS) may help overcome such barriers though past studies measuring Pb in DBS have been challenged with quality control, small sample volumes, and other issues. Total Reflection X-Ray Fluorescence (TXRF) may help address some of these challenges but has yet to be used to measure Pb in DBS. As such, the aim of the current study was to develop, validate, and apply a method to analyze Pb in DBS samples using TXRF for use in human biomonitoring studies. First, we developed a novel method (tested a range of parameters), and then used blood reference materials to validate the method against performance criteria listed in ICH Q2A and Q2B and the European Bioanalysis Forum. Finally, we applied the method to two populations who exemplify divergent conditions (41 university members with relatively low Pb exposures sampled in a clinical environment; 40 electronic waste workers with relatively high Pb exposures sampled in a contaminated field setting). The limits of detection and quantification of the method were 0.28 and 0.69 µg/dL, respectively. The overall precision and accuracy of the method were 15% and 111%, respectively. The mean (±SD) DBS Pb levels by TXRF in the university members and e-waste workers were 0.78 (±0.46) and 3.78 (±3.01) µg/dL, respectively, and these were not different from Pb measures in venous whole blood using ICP-MS. Bland-Altman plot analyses indicated good agreement between DBS Pb measures by TXRF versus whole blood Pb measures by ICP-MS in both groups. By combining data from the two population groups, there was no significant constant bias (intercept of 0.02 µg/dL) or proportional bias (slope was -0.02) between the two measures, and the lower and upper LoA were -0.86 and 0.91 µg/dL, respectively, with a LoA range of 1.77 µg/dL. These results demonstrate that TXRF-based analysis of Pb content in DBS is a good alternative to the gold standard (i.e., ICP-MS analysis of whole blood), and helps overcome some of the challenges associated with current methods.

Registration status, mercury exposure biomarkers, and neuropsychological assessment of artisanal and small-scale gold miners (ASGM) from the Western Region of Ghana.

The artisanal and small-scale gold mining (ASGM) sector is estimated to be the largest anthropogenic source of mercury pollution worldwide, and not surprisingly human exposures in this sector are amongst the highest of all population groups. While formalization of the sector has been proposed as a solution to help improve health and safety within ASGM sites, there are few empirical studies in support of this notion. The objective of this study was to assess if individuals working in ASGM sites that are registered have reduced mercury exposures and better neuropsychological scores than workers from unregistered sites. To achieve this objective, we studied biological samples (urine, hair) and survey data from a study of 404 ASGM workers (of which, 295 worked in registered ASGM sites) conducted in Tarkwa (Ghana) in 2014. Between miners working in registered and unregistered sites, there were few differences in socio-demographic characteristics. Median urinary mercury concentration (specific gravity-corrected) among those from unregistered mines was nearly 3-fold higher than those from the registered mines (18.5 versus 6.6 µg/L), and in the overall population the median concentration was 10.0 µg/L, and ranged from 0.3 to 2499 µg/L. Mercury biomarkers varied across ASGM work categories (e.g., those who burned or amalgamated had the highest) and users of personal protective equipment. Nearly 30% of the study population indicated having some challenges concerning, for example, reduced appetite, hair loss, or excess salivation. Ataxia and rigidity of gait were absent in most of the participants, and for those with slight, moderate, or marked responses, there were no differences between miners from registered and unregistered sites, across work groups, as well as in reference to mercury biomarker measures. For the pencil tapping, Frostig, matchbox, and Wechsler tests, no striking differences were found though a correlation was found between urinary mercury levels and matchbox scores among those who amalgamate and burn, and scores were similar to past studies using the same tests in ASGM sites. We believe this is the first study to compare mercury exposures and neuropsychological test results between miners from registered and unregistered ASGM sites. In doing so, the research findings provide the necessary evidence for stakeholders and parties of the Minamata Convention considering various response options to help fulfill their obligations.

Variation in biomarker levels of metals, persistent organic pollutants, and omega-3 fatty acids in association with genetic polymorphisms among Inuit in Nunavik, Canada.

BACKGROUND: Biomarker measures of contaminant exposure and nutrient status can help increase understanding of the risks and benefits associated with the consumption of traditional foods by Inuit. While gene-environment and gene-nutrient interactions may help explain variations in biomarker measures, the role of genetic polymorphisms is largely understudied especially for vulnerable sub-populations. OBJECTIVE: The aim of this study was to characterize the relationship between single nucleotide polymorphisms (SNPs) in key genes and blood concentrations of environmental chemicals and nutrients among Inuit. METHODS: Blood samples from 665 individuals who participated in the Qanuippitaa Survey (Nunavik, Canada) in 2004 were analyzed for toxicants and nutrients. DNA was extracted and 140 SNPs in classes relevant to the toxicokinetics and/or toxicodynamics of the target contaminants and nutrients, and/or are involved in cardiovascular health and lipid metabolism were genotyped using the Sequenom iPLEX Gold platform. RESULTS: Geometric means (µg/L) of mercury (Hg), cadmium (Cd), lead (Pb), DDE, PCB-153, and selenium (Se) were 11.1, 2.8, 39.9, 2.9, 1.1 and 301.2, respectively. Red blood cell membrane levels of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were 5.1%/total fatty acid (TFA) and 1.3%/TFA respectively. Out of 106 SNPs which met our inclusion criteria, biomarker levels for Hg, Cd, Pb, DDE, PCB-153, DHA, and EPA differed (p < 0.05) by genotype for 20, 13, 12, 19, 21, 9 and 8 SNPs, respectively. Following Bonferroni correction (p < 0.0005), only 9 SNPs remained significant (rs2274976 in MTHFR, rs174602 in FADS2, rs7115739 and rs74771917 in FADS3, rs713041 in GPX4, rs2306283 and rs4149056 in SLCO1B1, rs1885301 in ABCC2/MRP2, and rs4244285 in CYP2C19; 5 associated with Hg, 2 with Pb, 2 with DDE, 4 with PCB-153, 1 with DHA). CONCLUSIONS: The findings suggest that polymorphisms in environmentally-responsive genes can influence biomarker levels of key toxicants and nutrients. While there are no immediate clinical or public health implications of these findings, we believe that such gene-environment and gene-nutrient studies provide a foundation that will inform and provide direction to future studies.

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis.

The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) networks. It was soon updated for gene expression meta-analysis with improved workflow and performance. Over the years, NetworkAnalyst has been continuously updated based on community feedback and technology progresses. Users can now perform gene expression profiling for 17 different species. In addition to generic PPI networks, users can now create cell-type or tissue specific PPI networks, gene regulatory networks, gene co-expression networks as well as networks for toxicogenomics and pharmacogenomics studies. The resulting networks can be customized and explored in 2D, 3D as well as Virtual Reality (VR) space. For meta-analysis, users can now visually compare multiple gene lists through interactive heatmaps, enrichment networks, Venn diagrams or chord diagrams. In addition, users have the option to create their own data analysis projects, which can be saved and resumed at a later time. These new features are released together as NetworkAnalyst 3.0, freely available at https://www.networkanalyst.ca.

Global DNA (LINE-1) methylation is associated with lead exposure and certain job tasks performed by electronic waste workers.

OBJECTIVE: This study assessed the associations between blood and urine levels of toxic metals; cadmium (Cd) and lead (Pb), and methylation levels of the LINE-1 gene among e-waste and control populations in Ghana. METHODS: The study enrolled 100 male e-waste workers and 51 all-male non-e-waste workers or controls. The concentrations of Cd and Pb were measured in blood and urine using inductively coupled plasma mass spectrometry, while LINE1 methylation levels were assessed by pyrosequencing of bisulfite-converted DNA extracted from whole blood. Single and multiple metals linear regression models were used to determine the associations between metals and LINE1 DNA methylation. RESULTS: Blood lead (BPb) and urine lead (UPb) showed higher median concentrations among the e-waste workers than the controls (76.82 µg/L vs 40.25 µg/L, p ≤ 0.001; and 6.89 µg/L vs 3.43 µg/L, p ≤ 0.001, respectively), whereas blood cadmium (BCd) concentration was lower in the e-waste workers compared to the controls (0.59 µg/L vs 0.81 µg/L, respectively, p = 0.003). There was no significant difference in LINE1 methylation between the e-waste and controls (85.16 ± 1.32% vs 85.17 ± 1.11%, p = 0.950). In our single metal linear regression models, BPb was significantly inversely associated with LINE1 methylation in the control group (ßBPb = - 0.027, 95% CI - 0.045, - 0.010, p = 0.003). In addition, a weak association between BPb and LINE1 was observed in the multiple metals analysis in the e-waste worker group (ßBPb = - 0.005, 95% CI - 0.011, 0.000, p = 0.058). CONCLUSION: Continuous Pb exposure may interfere with LINE1 methylation, leading to epigenetic alterations, thus serving as an early epigenetic marker for future adverse health outcomes.

Personal exposure to particulate matter and heart rate variability among informal electronic waste workers at Agbogbloshie: a longitudinal study.

BACKGROUND: Informal electronic waste recycling activities are major contributors to ambient air pollution, yet studies assessing the effects or relationship between direct/continuous exposure of informal e-waste workers to particulate matter and cardiovascular function are rare. METHODS: Repeated measurements of fractions of PM2.5, PM10-2.5, and PM10 in personal air of informal e-waste workers, (n = 142) and a comparable group (n = 65) were taken over a period of 20 months (March 2017 to November, 2018). Concurrently, 5-min resting electrocardiogram was performed on each participant to assess resting heart rate variability indices. Linear mixed-effects models were used to assess the association between PM fractions and cardiac function. RESULTS: SDNN, RMSSD, LF, HF and LH/HF ratio were all associated with PM. Significant associations were observed for PM2.5 and Mean NN (p = 0.039), PM10 and SDNN (p = 0.035) and PM 10-2.5 and LH/HF (p = 0.039). A 10 µg/m3 increase in the concentrations of PM 2.5, PM10-2.5, and PM10 in personal air was associated with reduced HRV indices and increased resting HR. A 10 µg/m3 per interquartile (IQR) increase in PM10-2.5 and PM10, decreased SDNN by 11% [(95% CI: - 0.002- 0.000); (p = 0.187)] and 34% [(95% CI: - 0.002-0.001); (p = 0.035)] respectively. However, PM2.5 increased SDNN by 34% (95% CI: - 1.32-0.64); (p = 0.493). Also, 10 µg/m3 increase in PM2.5, PM10-2.5 and PM10 decreased RMSSD by 27% [(- 1.34-0.79); (p = 0.620)], 11% [(- 1.73, 0.95); (p = 0.846)] and 0.57% [(- 1.56-0.46); (p = 0.255%)]. CONCLUSION: Informal e-waste workers are at increased risk of developing cardiovascular disease from cardiac autonomic dysfunction as seen in reduced HRV and increased heart rate.

Mercury Speciation in Whole Blood and Dried Blood Spots from Capillary and Venous Sources.

There is interest in measuring total mercury (THg) and methylmercury (MeHg) in dried blood spots (DBS) though more research is required to evaluate mercury (Hg) speciation in DBS and to validate the agreement between blood sources (venous vs capillary) and matrices (whole blood vs DBS). Therefore, the present study aimed to develop, evaluate, and validate a DBS-based method to assess MeHg and inorganic mercury (InHg) exposure in human population studies. First, we used volume-controlled (40 µL) paired DBS-whole blood samples to develop an analytical method that involved the extraction and quantification of MeHg and InHg with gas chromatography-cold vapor atomic fluorescence spectrometry (GC-CVAFS). Next, we carried out a validation study using paired DBS-whole blood samples from venous and capillary sources from 49 volunteers with Hg exposures similar to background populations (i.e., MeHg in venous whole blood ranged from 0.2 to 3 µg/L with a median value of 0.8). The limits of detection were higher for InHg (1.9 and 1.1 µg/L in DBS and whole blood, respectively) than MeHg (0.3 and 0.2 µg/L in DBS and whole blood, respectively). The MeHg concentrations among blood sources and matrices were highly correlated (r ranged from 0.85 to 0.95), with no constant bias (intercept ranged from -0.05 to 0.13 µg/L) and small proportional bias (slopes ranged from 0.92 to 1.08). Bland-Altman plots indicated little bias between MeHg measurements with 82-98% of the cases meeting the analytical acceptance criterion of 35% maximum allowed difference. Our results indicate that measures of MeHg in capillary DBS reflect concentrations in the gold standard (i.e., venous whole blood) and that DBS is a suitable tool for assessing MeHg exposure in human population studies, but that more work is required to assess InHg exposures.

EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species.

Traditional results from toxicogenomics studies are complex lists of significantly impacted genes or gene sets, which are challenging to synthesize down to actionable results with a clear interpretation. Here, we defined two sets of 21 custom gene sets, called the functional and statistical EcoToxModules, in fathead minnow (Pimephales promelas) to (1) re-cast predefined molecular pathways into a toxicological framework and (2) provide a data-driven, unsupervised grouping of genes impacted by exposure to environmental contaminants. The functional EcoToxModules were identified by re-organizing KEGG pathways into biological processes that are more relevant to ecotoxicology based on the input from expert scientists and regulators. The statistical EcoToxModules were identified using co-expression analysis of publicly available microarray data (n = 303 profiles) measured in livers of fathead minnows after exposure to 38 different conditions. Potential applications of the EcoToxModules were demonstrated with two case studies that represent exposure to a pure chemical and to environmental wastewater samples. In comparisons to differential expression and gene set analysis, we found that EcoToxModule responses were consistent with these traditional results. Additionally, they were easier to visualize and quantitatively compare across different conditions, which facilitated drawing conclusions about the relative toxicity of the exposures within each case study.

Mercury exposure in relation to sleep duration, timing, and fragmentation among adolescents in Mexico City.

INTRODUCTION: Mercury intoxication is known to be associated with adverse symptoms of fatigue and sleep disturbances, but whether low-level mercury exposure could affect sleep remains unclear. In particular, children may be especially vulnerable to both mercury exposures and to poor sleep. We sought to examine associations between mercury levels and sleep disturbances in Mexican youth. METHODS: The study sample comprised 372 youth from the Early Life Exposures to Environmental Toxicants (ELEMENT) cohort, a birth cohort from Mexico City. Sleep (via 7-day actigraphy) and concurrent urine mercury were assessed during a 2015 follow-up visit. Mercury was also assessed in mid-childhood hair, blood, and urine during an earlier study visit, and was considered a secondary analysis. We used linear regression and varying coefficient models to examine non-linear associations between Hg exposure biomarkers and sleep duration, timing, and fragmentation. Unstratified and sex-stratified analyses were adjusted for age and maternal education. RESULTS: During the 2015 visit, participants were 13.3 ± 1.9 years, and 48% were male. There was not a cross-sectional association between urine Hg and sleep characteristics. In secondary analysis using earlier biomarkers of Hg, lower and higher blood Hg exposure was associated with longer sleep duration among girls only. In both boys and girls, Hg biomarker levels in 2008 were associated with later adolescent sleep midpoint (for Hg urine in girls, and for blood Hg in boys). For girls, each unit log Hg was associated with 0.2 h later midpoint (95% CI 0 to 0.4), and for boys each unit log Hg was associated with a 0.4 h later sleep midpoint (95% CI 0.1 to 0.8). CONCLUSIONS: There were mostly null associations between Hg exposure and sleep characteristics among Mexican children. Yet, in both boys and girls, higher Hg exposure in mid-childhood (measured in urine and blood, respectively) was related to later sleep timing in adolescence.

In utero and peripubertal metals exposure in relation to reproductive hormones and sexual maturation and progression among boys in Mexico City.

BACKGROUND: Endocrine disrupting chemicals (EDCs) such as metals have been reported to alter circulating reproductive hormone concentrations and pubertal development in animals. However, the relationship has rarely been investigated among humans, with the exception of heavy metals, such as Pb and Cd. Our aim was to investigate measures of in utero and peripubertal metal exposure in relation to reproductive hormone concentrations and sexual maturation and progression among boys from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohorts. METHODS: Our analysis included 118 pregnant women and their male children from the ELEMENT study. Essential and non-essential metals were measured in urine collected from the mothers during the third trimester of pregnancy and their male children at 8-14 years. Reproductive hormone concentrations [serum testosterone, estradiol, dehydroepiandrosterone sulfate (DHEA-S), inhibin B, and sex hormone-binding globulin (SHBG)] were measured in blood samples from the children at 8-14 years. We also assessed Tanner stages for sexual maturation (genital, pubic hair development, and testicular volume), at two time points (8-14, 10-18 years). We used linear regression to independently examine urinary metal concentrations in relation to each peripubertal reproductive hormones adjusting for child age and BMI. Generalized estimation equations (GEEs) were used to evaluate the association of in utero and peripubertal metal exposures with sexual maturation and progression during follow-up based on Tanner staging and testicular volume. RESULTS: In utero and prepubertal concentrations of some urinary metals were associated with increased concentrations of peripubertal reproductive hormones, especially non-essential metal(loid)s As and Cd (in utero), and Ba (peripubertal) as well as essential metal Mo (in utero) in association with testosterone. More advanced pubic hair developmental stage and higher testicular volume at the early teen visit was observed for boys with higher non-essential metal concentrations, including in utero Al and peripubertal Ba, and essential metal Zn concentration (peripubertal). These metals were also associated with slower pubertal progression between the two visits. CONCLUSION: These findings suggest that male reproductive development may be associated with both essential and non-essential metal exposure during in utero and peripubertal windows.